Score:0

'Segmentation fault (core dumped)'. What should I do to fix this error?

fr flag

I was going to do secondary structure analysis (of protein) by using 'gmx do_dssp' module (I use Gromacs package). 'Segmentation fault' occurred after I gave the command line - gmx do_dssp -f native.xtc -s md.tpr -map and I couldn’t get the outputs that were so important. What should I do to fix this error?

  • My current ubuntu version is 20.04
  • Gromacs is a package that used for running molecular dynamic simulations. In this package, all command lines begins with gmx. In this here gmx do_dssp .... is a command for which had to give me required information.
  • Before, such an error didn't occurred with ubuntu 18.04 .
  • All commands except for gmx do_dssp works well (Gromacs isn't broken installed). That is, the problem is only with this command.
N0rbert avatar
zw flag
What is your Ubuntu version? What is `gmx`? How did you installed it and which version?
Knud Larsen avatar
by flag
Ref. question : "Gromacs package" → `/usr/bin/gmx` https://packages.ubuntu.com/focal/amd64/gromacs/filelist
waltinator avatar
it flag
"`Segmentation fault`" is the Unix/Linux way of saying "Illegal Memory Access". Your program tried to access an out-of-bounds memory address. Experience suggests location `0x00`. The rest of the message "`(core dumped)`" is good news! A long, detailed report has been written to a file in the `/var/crash/` directory. Read it with `less` or `more`. Are you missing a library? That could cause a jump to `0x00`. Look at `ldd $(type -p gmx)`.
waltinator avatar
it flag
Please [edit] your post to add new information, properly formatted. Information added via comments is hard for you to format, hard for us to read and ignored by future readers. Please click [edit] and add that vital information to your question so all the facts we need are in the question. Please don't use Add Comment, since that's our uplink to you. All facts about your system should go in the Question with [edit]
heynnema avatar
ru flag
Go to https://www.memtest86.com/ and download/run their free `memtest` to test your memory. Get at least one complete pass of all the 4/4 tests to confirm good memory. This may take many hours to complete. Report back. Start comments to me with @heynnema or I'll miss them.
mangohost

Post an answer

Most people don’t grasp that asking a lot of questions unlocks learning and improves interpersonal bonding. In Alison’s studies, for example, though people could accurately recall how many questions had been asked in their conversations, they didn’t intuit the link between questions and liking. Across four studies, in which participants were engaged in conversations themselves or read transcripts of others’ conversations, people tended not to realize that question asking would influence—or had influenced—the level of amity between the conversationalists.